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Table 4 The dichotomy of the sentence expression for pathway representation: direct or indirect.

From: New challenges for text mining: mapping between text and manually curated pathways

reaction ID reaction type expected annotation class direct (annotated) indirect (not annotated)
R1 Binding Binding 11 56
R2 Binding Binding 16 20
R3 phosphorylation Protein_amino_acid_phosphorylation 19 1
+ site information Protein_amino_acid_phosphorylation 2 5  
+ modifier information + (any) Regulation 4 1  
R4 ubiquitination Protein_ubiquitination 5 0
R5 degradation Protein_catabolism 27 1
  + modifier information + (any) Regulation 6 3
R6 translocation Localization 26 0
R7 Binding Binding 23 12
R8 gene expression Gene_expression (or Transcription + Translation) 5 9
R9 gene expression Gene expression (or Transcription + Translation) 1 10
R10 processing Protein_processing 5 12
   total 150 130
  1. The sentences for pathway representation of each reaction were distributed by a direct or indirect expression. The direct expressions were annotated by ‘expected annotation class’ using GENIA event annotation, while the indirect expressions were not. The latter needs some ‘inference’ by the biological domain knowledge to construct the corresponding pathway.
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